Script for t2 based tests finished. Consider speeding up tests

Author: fabriciocravo

NBS_addon/NBSstats_smn.m

@@ -451,7 +451,6 @@
             flat_target_stat = flat_matrix(target_stat, STATS.mask);
             % Calculate p-values directly for each element in flat_target_stat
             pval = arrayfun(@(stat) sum(stat <= null_dist) / K, flat_target_stat);
-            disp('Place holder')
 
         case {3, 4, 5} % cNBS and SEA
 

atlas_storage/test_hcp_fc_atlas.mat

@@ -40,8 +40,6 @@ function create_t2_test_dataset()
     file_name = './data/test_t2_fc.mat';
 
     save(file_name, 'brain_data', 'study_info', 'outcome');
-    
-    %% Remove this later
-    edge_based_tests('test_t2_fc.mat')
+   
 
 end

create_t2_test_dataset.m

@@ -26,6 +26,11 @@
 test_power_calculation_from_gt_and_data()
 
 %% Create t2-test dataset 
+create_t2_test_dataset()
+
+edge_based_tests('test_t2_fc.mat')
+
+network_based_tests('test_t2_fc.mat')
 
 
 

power_calculator_test_script.m

@@ -5,8 +5,7 @@ function edge_based_tests(data_set_name)
 
     Params = common_test_setup(data_set_name);
 
-    % stat_method_cell = {'Parametric_Bonferroni', 'Parametric_FDR', 'Size', 'TFCE'};
-    stat_method_cell = {'Parametric_Bonferroni'};
+    stat_method_cell = {'Parametric_Bonferroni', 'Parametric_FDR', 'Size', 'TFCE'};
 
     Params.all_cluster_stat_types = stat_method_cell;
 

test_scripts/edge_based_tests.m

@@ -1,5 +1,8 @@
 function network_based_tests(data_set_name)
 
+    data_set = load(['./data/', data_set_name]);
+    data_set_name = get_data_set_name(data_set);
+
     Params = common_test_setup(data_set_name);
 
     stat_method_cell = {'Constrained', 'Constrained_FWER'};
@@ -13,7 +16,7 @@ function network_based_tests(data_set_name)
         method = stat_method_cell{i};
 
         % The query is based on how the dataset is created
-        query = {'testing', 'test_hcp', 'REST_TASK', method, 'subs_40', 'brain_data'};
+        query = {'testing', data_set_name, 'REST_TASK', method, 'subs_40', 'brain_data'};
 
         brain_data = getfield(ResData, query{:});